One of Washington's most wanted al-Qaida fugitives was captured in Karachi in July and secretly transferred to US custody, striking a significant blow to Osama bin Laden's network, Pakistani intelligence sources have claimed.

Sheikh Ahmed Salim, detained in a joint Pakistan-US raid, was among a group of suspects flown out of the country in recent weeks.

The 33-year-old Kenyan, who also goes by the name Swedan, had a $25m (£16m) price on his head for his role in the 1998 bombings of US embassies in east Africa. Since then he is believed to have emerged as an important al-Qaida figure, directing and funding Islamist militants in Pakistan.

Officially, the Pakistani and US governments denied knowledge of the arrest, but in interviews with the Guardian, senior Pakistani intelligence sources and a top investigator in Karachi insisted they had positively identified Salim among suspects arrested in a raid in Karachi in July.

Details of the arrest emerged as Guardian reporters in 11 countries were preparing an in vestigation into the strength of al-Qaida internationally, a year after the September 11 attacks. Their research reveals new information on how Bin Laden slipped away from US forces in Afghanistan; produces evidence connecting a deadly attack on a synagogue in Tunisia this year with al-Qaida; and shows how al-Qaida operatives are using local groups in Pakistan to organise a new wave of attacks on foreigners.

Pakistani intelligence agents were led to Salim's cell by satellite telephone intercepts provided by the FBI. That led to the arrest in Karachi of a more junior al-Qaida figure, a Saudi known only as Riyadh or Riaz. In early July he in turn led investigators to Salim, who was arrested in Kharadar, a slum area in the south of the city.

Salim, who once ran a trucking firm in Kenya, is alleged to have bought the Toyota and Nissan lorries used in the 1998 embassy attacks in Nairobi and Dar es Salaam, before fly ing out of Nairobi to Karachi five days before the assault was launched.

Asked about Salim's arrest yesterday, a US intelligence official said he had "nothing to substantiate" the report. The Pentagon has a policy of not naming suspects in military custody, to keep al-Qaida guessing about how much the US knows.

Salim told Pakistani investigators that he had collected millions of dollars from local sympathisers in the months since September 11. His claims were regarded as exaggerated but thousands of dollars and fake passports and visa stamps were found in his house. He is believed to have worked in particular with Pakistani militants from the banned Lashkar-i-Jhangvi group. After a series of arrests of Lashkar members in Karachi police found a makeshift chemical laboratory which contained several toxins, including cyanide.

Islamists have already launched attacks against western targets in Pakistan which it is believed were coordinated by al-Qaida. In May a suicide bomber killed 11 French engineers outside the Sheraton hotel in Karachi. A month later a second suicide bomber crashed a van into the US consulate, killing 10 Pakistanis.